On wavelet-based features for classifying mass spectrometry data

Outline

Introduction
Related Work
Methods
Results
Conclusions

Introduction

High dimensional data refers to data with large number of features (co-variates) \(p\), formally we can write data is \(\mathbf{X} \in \mathbb{R} ^{n\times p}\):

\[ p \gg n, \tag{1} \] where \(n\) is the number of observations.

Introduction

In this context, many challenges arise:

Sparse Data
Overfitting
Feature Redundancy and Correlation
Increased Training and Modeling time
Difficultly in Visualization
Class Imbalance
Noisy Features
…

Introduction

Some solutions in the literature:

Principal Component Analysis (PCA) (Jolliffe 2002),
t-Distributed Stochastic Neighbor Embedding (t-SNE) (Maaten and Hinton 2008)
Uniform Manifold Approximation and Projection (UMAP) (McInnes, Healy, and Melville 2020)
Regularizations such as \(L1\) (Lasso) (Tibshirani 1996) and \(L2\) (Ridge, Tikhonov) (Hoerl and Kennard 1970)
Feature Selection such as mutual information (Fleuret 2004)

The problem in hand

Our data is a mass spectrum signal data (functional data).

\(p >90000\) features or dimensions and \(p <100\) subjects or observations

Our goal is develop a methodology to classify the functional data, such as cancer mass spectrum data (Cancer is the second leading cause of death in the world after heart disease)
Our focus is to leverage the capabilities of Wavelet Analysis.

Wavelet Analysis

The Fourier Transform of a signal \(x(t)\) can be expressed as:

\[ X(f)= \int_{-\infty}^{\infty} x(t) e^{i2 \pi ft} dt \tag{2} \](\(e^{ix}= \cos x + i \sin x\), Euler’s formula); \(f\) is the frequency domain.

The Wavelet Transform of a signal \(x(t)\) can be given as:

\[ WT(s,\tau)= \frac{1}{\sqrt s}\int_{-\infty}^{\infty} x(t) \psi^*\big(\frac{t-\tau}{s}\big) dt, \tag{3} \]

where \(\psi^*(t)\) denotes the complex conjugate of the base wavelet \(\psi(t)\)); \(s\) is the scaling parameter, and \(\tau\) is the location parameter.

Example: Morlet Wavelet \(\psi(t) = e^{i2 \pi f_0t} e^{-(\alpha t^2/\beta^2)}\), with the parameters \(f_0\), \(\alpha\), \(\beta\) all being constants.

Wavelet Families

Discrete Wavelet Transform

Related Work

Ovarian cancer detection (Yu et al. 2005): A combination of Binning, Kolmogorov-Smirnov test, discrete wavelet transform, and support vector machines.
Proteomic profile with bi-orthogonal discrete wavelet transform (Schleif et al. 2009): A combination of outlier detection-centroied-based, recalibration, baseline correction (top-hat filter), Kolmogorov-Smirnov test, discrete wavelet transform bior 3.7, and support vector machines.
Ovarian cancer detection using peaks and discrete wavelet transform (Du et al. 2009): A combination of discrete wavelet transform, thresholding, peak detection using MAD, Kolmogorov-Smirnov test, bagging predictor.

Related Work

Ovarian cancer classification using wavelets and genetic algorithm (Nguyen et al. 2015): A combination of Haar discrete wavelet transform, genetic algorithms.
Breat cancer mass spectrum classification (Cohen, Messaoudi, and Badir 2018): A combination of segmentation, discrete wavelet transform, statistical features on the coefficients, PCA-T2 Hotelling statistic, SVM.
Ovarian cancer mass spectrum classification (Vimalajeewa, Bruce, and Vidakovic 2023): A combination of Daubechies-7 wavelet transform, sample variance and distance variance, Fisher’s criterion for feature extraction, SVM, KNN, and Logistic regression.

Methods

A workflow for ML is the following:

Data Collection
Data Processing: Clean, Explore, Prepare, Transform
Modeling: Develop, Train, Validate, and Evaluate,
Deployment: Deploy, Monitor and Update
Go to 1.

We designed a statistical experiment to evaluation 4 different processing approaches.

Methods

Variables of the experimental design:

Four pre-processing techniques.
- 5 window sizes.
- Two are wavelet-based and two are not.
- 10 wavelets families
Four ML Models: Logistic Regression, Support Vector Machine, Random Forest, and XGboost.
Two sampling: up and down sampling to overcome the imbalance classes
Repeat 100 times each case.

A total of 88000 models were run.

Methods

Processing 1 (PROC1): The feature space includes mean, variance, energy, coefficient of variation, Skewness, and Kurtosis; wavelet transform.
Processing 2 (PROC2): Same as PROC1 but the feature space will include the first 10 autocorrelation coefficients.
Processing 3 (PROC3): Same as PROC1 but without the wavelet transform.
Processing 4 (PROC4): Same as PROC2 but without the wavelet transform.

Methods

The performance metrics utilized were:

Recall
Precision
F1-score
Accuracy

Data sets

Low-mass range SELDI spectra
- 50 cancer
- 30 normal

Observed 32,768 m/z values / 33,885 m/z values

Link: https://bioinformatics.mdanderson.org/public-datasets/

Results

Performance across Processing

Characteristic	PROC1		PROC2		PROC3		PROC4
Characteristic	Downsample N = 20,000¹	Upsample N = 20,000¹	Downsample N = 20,000¹	Upsample N = 20,000¹	Downsample N = 2,000¹	Upsample N = 2,000¹	Downsample N = 2,000¹	Upsample N = 2,000¹
precision	0.70 ± 0.10 (0.40,1.00)	0.70 ± 0.10 (0.40,1.00)	0.71 ± 0.12 (0.40,1.00)	0.71 ± 0.12 (0.40,1.00)	0.78 ± 0.12 (0.57,1.00)	0.78 ± 0.12 (0.50,1.00)	0.73 ± 0.10 (0.50,1.00)	0.73 ± 0.10 (0.50,1.00)
recall	0.88 ± 0.16 (0.40,1.00)	0.88 ± 0.16 (0.40,1.00)	0.86 ± 0.17 (0.40,1.00)	0.86 ± 0.17 (0.40,1.00)	0.91 ± 0.12 (0.60,1.00)	0.91 ± 0.12 (0.60,1.00)	0.88 ± 0.17 (0.40,1.00)	0.88 ± 0.17 (0.40,1.00)
F1.score	0.77 ± 0.10 (0.40,1.00)	0.77 ± 0.10 (0.40,1.00)	0.77 ± 0.10 (0.40,1.00)	0.77 ± 0.11 (0.40,1.00)	0.83 ± 0.10 (0.60,1.00)	0.83 ± 0.10 (0.55,1.00)	0.79 ± 0.10 (0.44,0.91)	0.79 ± 0.10 (0.44,0.91)
accuracy	0.68 ± 0.13 (0.25,1.00)	0.68 ± 0.13 (0.25,1.00)	0.68 ± 0.13 (0.25,1.00)	0.68 ± 0.13 (0.25,1.00)	0.77 ± 0.13 (0.50,1.00)	0.77 ± 0.13 (0.38,1.00)	0.71 ± 0.12 (0.38,0.88)	0.71 ± 0.12 (0.38,0.88)
¹ Mean ± SD (Min,Max)

All PROC seems to perform similarly across ML techniques, etc.

Results

Performance across window sizes

References

Cohen, Achraf, Chaimaa Messaoudi, and Hassan Badir. 2018. “A New Wavelet-Based Approach for Mass Spectrometry Data Classification.” In New Frontiers of Biostatistics and Bioinformatics, edited by Yichuan Zhao and Ding-Geng Chen, 175–89. Cham: Springer International Publishing. https://doi.org/10.1007/978-3-319-99389-8_8.

Du, Jianqiang, Xiao-Min Wu, Bo Wang, Heng-Jie Su, Kai Ma, and Hu-Qin Zhang. 2009. “Wavelet Transform and Bagging Predictor Approaches to Cancer Identification from Mass Spectrometry-Based Proteomic Data.” In 2009 3rd International Conference on Bioinformatics and Biomedical Engineering, 1–4. IEEE.

Fleuret, François. 2004. “Fast Binary Feature Selection with Conditional Mutual Information.” Journal of Machine Learning Research 5: 1237–63.

Hoerl, Arthur E, and Robert W Kennard. 1970. “Ridge Regression: Biased Estimation for Nonorthogonal Problems.” Technometrics 12 (1): 55–67.

Jolliffe, I. T. 2002. Principal Component Analysis. 2nd ed. Springer.

Maaten, Laurens van der, and Geoffrey Hinton. 2008. “Visualizing High-Dimensional Data Using t-SNE.” Journal of Machine Learning Research 9: 2579–2605.

McInnes, Leland, John Healy, and James Melville. 2020. “UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction.” https://arxiv.org/abs/1802.03426.

Nguyen, Thanh, Saeid Nahavandi, Douglas Creighton, and Abbas Khosravi. 2015. “Mass Spectrometry Cancer Data Classification Using Wavelets and Genetic Algorithm.” FEBS Letters 589 (24): 3879–86.

Schleif, Frank-Michael, Mathias Lindemann, Mario Diaz, Peter Maaß, Jens Decker, Thomas Elssner, Michael Kuhn, and Herbert Thiele. 2009. “Support Vector Classification of Proteomic Profile Spectra Based on Feature Extraction with the Bi-Orthogonal Discrete Wavelet Transform.” Computing and Visualization in Science 12: 189–99.

Tibshirani, Robert. 1996. “Regression Shrinkage and Selection via the Lasso.” Journal of the Royal Statistical Society: Series B (Methodological) 58 (1): 267–88.

Vimalajeewa, Dixon, Scott Alan Bruce, and Brani Vidakovic. 2023. “Early Detection of Ovarian Cancer by Wavelet Analysis of Protein Mass Spectra.” Statistics in Medicine 42 (13): 2257–73.

Yu, J. S., S. Ongarello, R. Fiedler, X. W. Chen, G. Toffolo, C. Cobelli, and Z. Trajanoski. 2005. “Ovarian Cancer Identification Based on Dimensionality Reduction for High-Throughput Mass Spectrometry Data.” Bioinformatics 21 (10): 2200–2209. https://doi.org/10.1093/bioinformatics/bti370.